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Chunk #9 — Materials and Methods — SNP genotyping

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GABRR1 and GABRR2, encoding the GABA-A receptor subunits rho1 and rho2, are associated with alcohol dependence.
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Because HapMap data indicated that flanking genes were in LD with the GABRR1-GABRR2 gene cluster, we extended the genotyping into the flanking regions. Seventy three SNPs in a 262 kb region, including GABRR1 and GABRR2, UBE2J1 (ubiquitin-conjugating enzyme E2, J1) upstream of GABRR2, and PM20D2 (peptidase M20 domain containing 2), SRrp35 (serine-arginine repressor protein) and PNRC1 (proline-rich nuclear receptor coactivator 1) downstream of GABRR1 (Figure 1), were selected from public databases (dbSNP and HapMap). Preference was given to SNPs having minor allele frequencies greater than 5%. Four synonymous SNPs in the coding regions of GABRR1 and GABRR2 (rs34218666, rs35608866, rs34617047, and rs35301635) were genotyped despite their reported low minor allele frequencies; they proved monomorphic in our sample and are not included in the tables or analyses. SNP positions were obtained from NCBI reference human genome, build 36.3.